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Protein evidence derived from mass spectrometry (MS) across cancer cohorts and model systems is extensive but remains fragmented across individual studies and repositories, limiting rapid retrieval and evidence-based benchmarking of cancer-context protein detection. Here we …
Read PDFDNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from …
Read PDF<h4>Premise</h4>Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to …
Read PDFComplex congenital chromosome abnormalities are rare but often cause severe symptoms. However, the structures and biological impacts of such abnormalities have seldomly been analyzed at the molecular level. Previously, we reported a Japanese female patient …
Read PDFThe hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina …
Read PDF<h4>Background</h4>DNA sequence variation and altered epigenetic regulation of the oxytocin receptor gene (OXTR) have been implicated in autism and autistic-like behaviors. While previous studies have examined subsegments of OXTR, nanopore Cas9-targeted sequencing (nCATS) allows deep …
Read PDFEpigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple …
Read PDFEpitranscriptomics has emerged as a rapidly evolving field that focused on studying post-transcriptional RNA modifications and their role in spatiotemporal regulation of gene expression. N6-methyladenosine (m<sup>6</sup>A) and 5-methylcytosine (m<sup>5</sup>C) represent the most extensively studied modifications …
Read PDF<h4>Background</h4><i>Ogataea parapolymorpha DL-1</i> is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome …
Read PDFCpG methylation, a key epigenetic mark involved in gene regulation, development, and other biological processes, is commonly analyzed using Whole-Genome Bisulfite Sequencing (WGBS). However, bisulfite treatment causes significant DNA degradation. Enzymatic Methyl-seq (EM-seq) offers a …
Read PDF<h4>Background</h4>A subset of developmental disorders (DD) is characterized by disease-specific genome-wide methylation changes. These episignatures inform on the underlying pathogenic mechanisms and can be used to assess the pathogenicity of genomic variants as well as …
Read PDFWith ongoing improvements in the detection of complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of …
Read PDF<h4>Background</h4>The gene C9orf72 harbors a non-coding hexanucleotide repeat expansion known to cause amyotrophic lateral sclerosis and frontotemporal dementia. While previous studies have estimated the length of this repeat expansion in multiple tissues, technological limitations have …
Read PDF<h4>Background</h4>Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder with characteristic clinical features such as overgrowth and macroglossia. Hypermethylation of the H19/IGF2:IG-differentially methylated region (H19-DMR) is identified in 5% of BWS patients. Although defects in the OCT4/SOX2 …
Read PDFLong-read sequencing (LRS) is a promising technology positioned to study the significant proportion of rare diseases (RDs) that remain undiagnosed as it addresses many of the limitations of short-read sequencing, detecting and clarifying additional disease-associated …
Read PDF<h4>Background</h4>Imprinted genes are expressed in a parental-origin-specific manner. The imprinted regions including imprinted genes have differentially methylated regions (DMRs) with different 5-methylcytosine (5mC) patterns for CpGs on each parental allele, and DMRs function as imprinting …
Read PDF<h4>Background</h4>Non-invasive urine tests for bladder cancer (BC) could reduce dependence on flexible cystoscopy for diagnosis and surveillance. Most recent developments in urine testing are based on targeted detection of genomic and/or epigenomic markers. We hypothesised …
Read PDFCancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can …
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